Question: Depth of coverage of Bed file regions?
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gravatar for Jon17
9 weeks ago by
Jon1710
Jon1710 wrote:

Best way to find average depth of coverage for very specific regions via a bed file?

I've tried this: bedtools genomecov -i $BED -ibam $BAM

But my bam file says this:

chr1 69090 69190
chr1 69190 69290
chr1 69290 69390
chr1 69390 69490

and the output is this:

chr1 0 235026752 248956422 0.944048
chr1 1 4040485 248956422 0.0162297
chr1 2 983706 248956422 0.00395132
chr1 3 565978 248956422 0.0022734

which isn't helpful.

I'm hoping to get something similar to this:

chromosome Start stop Depth_of_coverage
chr1 69090 69190 45
chr1 69190 69290 46
chr1 69290 69390 45
chr1 69390 69490 30

genome coverage bed bedtools • 138 views
ADD COMMENTlink modified 9 weeks ago by h.mon25k • written 9 weeks ago by Jon1710
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